tbuckley/cabot-search huggingface dataset:
MDB-29. MEDULLOBLASTOMA SUBGROUP-SPECIFIC CHROMATIN STATES REVEAL NOVEL THERAPEUTIC VULNERABILITIES
Authors: Ran Tao, Qingsong Gao, Serap Erkek, Yurika Matsui, Nadhir Djekidel, Emily Darrow, Rahul Kumar, Kyle Smith, Gang Wu, Jan Korbel, Jamy Peng, Stefan Pfister, Paul Northcott
Journal: Neuro-Oncology (2023)

Abstract Medulloblastoma (MB) is a highly malignant childhood brain tumor comprising a collection of molecularly and clinically distinct entities. Mutations in chromatin-modifying genes distribute across subgroups and account for nearly half of all MBs. However, the molecular consequences of chromatin modifier alterations remain poorly understood. Herein, we characterize the chromatin landscape of fifty-two primary MBs representing each MB subgroup using chromatin immunoprecipitation followed by sequencing (ChIP-seq) for six histone marks and perform multi-layered integration with somatic genetics, genome-wide DNA methylation, and transcriptomic datasets extracted from the same tumors. Analysis of differential chromatin states across MB subgroups identified significant enrichment of a bivalent enhancer state (EnhBiv) in Group 4 MB. Group 4-specific EnhBivs mapped to promoters of key neurodevelopmental genes and transcription factors and was associated with increased DNA methylation and reduced expression. In accordance with higher EnhBivs coverage in Group 4 MB, we found that KDM2B, a H3K4me3 and H3K36me2 demethylase, is highly expressed in Group 4 MBs and patient-derived xenografts (PDXs). KDM2B knockout mediated by CRISPR targeting suppressed growth of both Group 3 MB cell lines in vitro and Group 4 MB PDXs in vivo but had no effect on control SHH-MB cells, suggesting that KDM2B is a novel selective dependency in MB. Knockout of KDM2B in MB cells induced profound upregulation of PRC2 targets, genes regulated by bivalent histone marks, as well as genes involved in neuronal differentiation. Further biochemical and molecular studies demonstrated that KDM2B interacts with PRC2 complex subunits and occupies gene promoters associated with Group 4-specific EnhBiv chromatin. In summary, our comprehensive characterization of the MB chromatin landscape in a large cohort of primary tumors provides novel insights into the epigenetic basis of MB and implicates KDM2B as a novel Group 4 MB dependency that should be prioritized as a therapeutic target in this subgroup.
MDB-18. MOLECULARLY-DEFINED MEDULLOBLASTOMA: POPULATION-LEVEL PATTERNS IN THE UNITED STATES, 2018-2019
Authors: Quinn T Ostrom, Mackenzie Price, Corey Neff, Gino Cioffi, Kristin A Waite, Carol Kruchko, Jill S Barnholtz-Sloan
Journal: Neuro-Oncology (2023)

Abstract Medulloblastoma is one of the most common types of brain and other CNS tumors among the pediatric population in the US. Molecularly-defined brain tumor histopathologies—including medulloblastoma subtypes—were incorporated into US cancer registry reporting for individuals with brain tumors beginning in 2018. We assessed the epidemiology and overall survival (OS) patterns for medulloblastoma in children and adolescents, highlighting molecularly-defined subtypes. Children and adolescents (0-19 years) that were histopathologically diagnosed with medulloblastoma from 2018-2019 and had brain molecular marker data were identified within the Commission on Cancer’s National Cancer Database (NCDB) and Central Brain Tumor Registry of the United States databases, which combines data from CDC’s National Program of Cancer Registries (NPCR) and NCI’s Surveillance, Epidemiology, and End Results (SEER) Programs. Incidence rates per 100,000 population with 95% confidence intervals (95CI) were estimated for histopathologies with ≥16 cases. One-year OS was estimated using NCDB data for histopathologies with ≥50 cases with follow-up through 2020 using Kaplan-Meier methods. There were 601 cases of histopathologically-confirmed medulloblastoma diagnosed in children and adolescents from 2018-2019, 39.6% of which had available molecular subtype information. Overall incidence of medulloblastoma was 0.37 (95CI=0.34-0.40). Incidence of medulloblastoma subtypes was 0.05 (95CI=0.04-0.06) for SHH-activated &amp; TP53wt, 0.02 (95CI=0.01-0.02) for WNT-activated, 0.08 (95CI=0.06-0.09) for nonWNT/nonSHH, while SHH-activated &amp; TP53mut was too rare to calculate incidence. One-year OS for all medulloblastoma was 96.6% (95CI=92.1%-100.0%). One-year OS for nonWNT/nonSHH was 96.6% (95CI=92.8%-100.0%), and for SHH-activated &amp; TP53wt was 93.7% (95CI=87.1%-100.0%). Other subtypes occurred too rarely to calculate survival. Our findings provide the initial US epidemiological estimates for molecularly-defined medulloblastoma histopathologies in children and adolescents. As improvements in collection completeness lead to increased molecular subtype availability, the robustness of these estimates will increase. Collection of these data are essential for understanding the epidemiology of this important childhood and adolescent brain tumor.
Arthroscopic capsular shift surgery in patients with atraumatic shoulder joint instability: a randomised, placebo-controlled trial
Authors: Anju Jaggi, Robert D Herbert, Susan Alexander, Addie Majed, David Butt, Deborah Higgs, Will Rudge, Karen A Ginn
Journal: British Journal of Sports Medicine (2023)

Objectives To determine the effect of arthroscopic capsular shift surgery on pain and functional impairment for people with atraumatic shoulder (glenohumeral) joint instability. Methods We conducted a randomised, placebo-controlled clinical trial in a specialist secondary care facility. Patients aged 18 years and over who reported insecurity (apprehension) in their shoulder joint and had evidence of capsulolabral damage on arthroscopic examination were included. Patients were excluded if their shoulder apprehension symptoms were precipitated by a high velocity shoulder injury, they had bony or neural damage, a rotator cuff or labral tear, or previous surgery on the symptomatic shoulder. Sixty-eight participants were randomised and received diagnostic arthroscopy, followed by arthroscopic capsular shift or diagnostic arthroscopy alone. All participants received the same postoperative clinical care. The primary outcome was pain and functional impairment measured with the Western Ontario Shoulder Instability Index. The prespecified minimum clinically important effect was a reduction in pain and disability of 10.4 points. Results Mean reductions in pain and functional impairment for both groups were similar. Compared with diagnostic arthroscopy, arthroscopic capsular shift increased pain and functional impairment by means of 5 points (95% CI −6 to 16 points) at 6 months, 1 point (95% CI −11 to 13 points) at 12 months and 2 points (95% CI −12 to 17 points) at 24 months. Conclusions Compared with diagnostic arthroscopy alone, arthroscopic capsular shift confers, at best, only minimal clinically important benefit in the medium term. Trial registration number NCT01751490 .
Defining Small Intestinal Bacterial Overgrowth by Culture and High Throughput Sequencing
Authors: Gabriela Leite, Ali Rezaie, Ruchi Mathur, Gillian M. Barlow, Mohamad Rashid, Ava Hosseini, Jiajing Wang, Gonzalo Parodi, Maria Jesus Villanueva-Millan, Maritza Sanchez, Walter Morales, Stacy Weitsman, Mark Pimentel, M.D. hristopher Almario, Benjamin Basseri, Yin Chan, Bianca Chang, Derek Cheng, Pedram Enayati, Srinivas Gaddam, Laith Jamil, Quin Liu, Simon Lo, Marc Makhani, Deena Midani, Mazen Noureddin, Kenneth Park, Shirley Paski, Nipaporn Pichetshote, Shervin Rabizadeh, Soraya Ross, Omid Shaye, Rabindra Watson, Ali Rezaie, Mark Pimentel
Journal: Clinical Gastroenterology and Hepatology (2023)
HGG-28. INTERIM ANALYSIS OF THE GCC1949 PHASE 2 TRIAL USING INDOXIMOD-BASED CHEMO-IMMUNOTHERAPY FOR PATIENTS WITH PEDIATRIC BRAIN TUMORS
Authors: Theodore S Johnson, Rafal Pacholczyk, Dolly Aguilera, Zuzana Berrong, Robert C Castellino, Susan Chi, Julianne Creager, Bree R Eaton, Jason R Fangusaro, Chenbin Huang, Trent Hummel, Lisa Ingerski, Eugene P Kennedy, Eric Ring, Ramses F Sadek, Sarthak Satpathy, Matthew Schniederjan, Beena E Thomas, Kee Kiat Yeo, Manoj Bhasin, Tobey J MacDonald, David H Munn
Journal: Neuro-Oncology (2023)

Abstract Brain tumors are the leading cause of cancer-related death in children. We report interim results of an ongoing multi-institutional phase 2 trial (NCT04049669) of the IDO pathway-inhibitor indoximod utilized in a chemo-immunotherapy regimen for patients 3-21 years of age with either recurrent malignant brain cancer or newly-diagnosed diffuse intrinsic pontine glioma (DIPG). Patients are treated with oral indoximod (38.4 mg/kg/day, divided BID) plus oral temozolomide (200 mg/m2/day for 5 days) in 28-day cycles. Patients for whom radiation therapy is planned as standard-of-care receive indoximod during the up-front radiation regimen. During treatment, palliative radiation, surgery, or dexamethasone are allowed as needed for clinical management. To date, 53 patients have been treated. Estimated median follow-up time was 23 months (range 0.2-35.5 months), and indoximod-based therapy was well tolerated. Estimated median overall survival (OS) was 15 months for the entire mixed population (n= 53, 95%-C.I. 11.5-23.2 months); 23.8 months for recurrent ependymoma (n=26); 13.5 months for recurrent medulloblastoma (n=12); 5.8 months for recurrent glioblastoma/diffuse midline glioma (GBM/DMG, n=9, excludes DIPG); and 9.6 months for newly-diagnosed DIPG (n=6). For the 39 response-evaluable patients to date (those with measurable disease and at least one follow-up MRI on-therapy), objective response in any single lesion by pediatric RANO criteria occurred in 20/39 patients (9/17 ependymoma, 9/11 medulloblastoma, 0/6 GBM/DMG, 2/5 DIPG). Lesion response was associated with significantly better overall survival (estimated median OS 23.2 months, n=20) compared to patients without lesion response (median OS 6.6 months, n=19) (p=0.0005). Single-cell RNA sequencing of serial peripheral blood samples allowed identification of expanded T cell clones, which was correlated with survival. Updated results from the first 53 patients will be presented. These data are replicating results of the preceding phase 1 study (NCT02502708) and provide preliminary evidence of anti-tumor activity in pediatric brain tumors.
ATRT-10. SINGLE-CELL TRANSCRIPTOME ANALYSIS REVEALS CELLULAR HIERARCHIES AND THERAPEUTIC VULNERABILITIES OF ETMR
Authors: Alexander Beck, Lisa Gabler, Gustavo A V Cruzeiro, Sander Lambo, Bernhard Englinger, McKenzie L Shaw, Olivia A Hack, Ilon Liu, Carlos A O de Biagi Junior, Rebecca D Haase, Marbod Klenner, Pia Freidel, Sibylle Madlener, Lisa Mayr, Daniel Senfter, Andreas Peyrl, Irene Slavc, Daniela Lötsch, Christian Dorfer, Christine Haberler, Stefan M Pfister, Lissa Baird, Susan N Chi, Sanda Alexandrescu, Johannes Gojo, Marcel Kool, Volker Hovestadt, Mariella G Filbin
Journal: Neuro-Oncology (2023)

Abstract Embryonal tumors with multilayered rosettes (ETMR) are malignant brain tumors that occur predominantly in infants and young children. Most patients die within two years of diagnosis, and more effective, targeted therapies are urgently needed. To better characterize the oncogenic mechanisms of key driver alterations and to identify novel therapeutic targets, we set out to study the cellular heterogeneity of ETMR using single-cell RNA sequencing. Analyses conducted on &amp;gt;4,000 high-quality cells collected from eleven primary and relapse specimens revealed a common cellular hierarchy across all tumors: A highly proliferative neural stem cell-like population (SOX2+) that gives rise to intermediate progenitors (NEUROD1/NEUROG1+) and more differentiated neuron-like cells (STMN2/4+). These malignant cell populations closely overlap with histological patterns of ETMRs, as confirmed by multiplexed immunofluorescence microscopy on patients’ tumors. Comparison to single-cell datasets from human fetuses indicated high resemblance to normal cortical neurogenesis but also revealed key tumor-specific differences. These include expression of the chromosome 19 miRNA cluster (C19MC, the presumed driver in ~90% of ETMRs), which was restricted to the malignant stem cell-like population. Investigating oncogenic mechanisms of C19MC (comprising 46 miRNA genes) through transcriptome-wide RNA immunoprecipitation analysis, we identified extensive target gene regulation for most C19MC members, including distinct regulators of cell cycle, pluripotency, and neuronal differentiation. Silencing of C19MC families with antisense oligonucleotides resulted in pronounced reduction of ETMR cell line growth, indicating potential avenues for therapeutic targeting in the future. To identify more immediately actionable targets, we investigated inter-cellular signaling between malignant cell populations of ETMRs. Interestingly, we identified marked FGFR and NOTCH receptor-ligand interactions common to all tumors. An in vitro screen of experimental and approved small molecule inhibitors designed to target these interactions nominated several promising candidates for clinical evaluation. Our unpublished results provide much needed insight into targeting ETMR cellular states using multiple modes of action.
LGG-09. CLINICAL ACTIVITY OF PAN-RAF INHIBITOR TOVORAFENIB IN THE REGISTRATIONAL PEDIATRIC LOW-GRADE GLIOMA ARM OF THE PHASE 2 FIREFLY-1 (PNOC026) STUDY
Authors: Lindsay Kilburn, Dong-Anh Khuong-Quang, Karsten Nysom, Daniel Landi, David Ziegler, Pablo Hernáiz Driever, Sarah Leary, Simon Bailey, Jasper Van der Lugt, Sebastien Perreault, Angela Waanders, Patricia Baxter, Olaf Witt, Darren Hargrave, Geoffrey McCowage, Xin Zhao, Daniel Da Costa, Michael Cox, Peter Manley, Jordan Hansford
Journal: Neuro-Oncology (2023)

Abstract Genomic alterations of BRAF are common oncogenic drivers in pediatric low-grade glioma (pLGG). Tovorafenib is an investigational, oral, selective, brain-penetrant, small molecule, type II panRAF inhibitor. FIREFLY-1 (NCT04775485) is a multicenter phase 2 study evaluating the efficacy and safety of tovorafenib monotherapy in patients with BRAF-altered cancers. Registrational arm 1 includes patients 6 months-25 years of age with recurrent or progressive LGG previously treated with ≥1 prior line of systemic therapy. Tovorafenib 420 mg/m2 (≤600 mg) is administered weekly, in 28-day cycles, (tablet or liquid suspension formulation) until progression. The primary endpoint of arm 1 is ORR, as defined by RANO criteria and determined by blinded independent review. As of September 28, 2022, arm 1 had enrolled 77 patients and is fully accrued. All patients had ≥6 months of follow-up. Median age at enrollment was 8 years (range 2-21). Patients had received a median of 3 prior lines of systemic therapy (range: 1-9); 60% had received prior MAPK pathway-targeted agents. The most common tumor site was optic pathway (51%). Sixty-four patients harbored a tumor BRAF fusion/rearrangement (83%) and 13 (17%) a V600E mutation. Median duration of tovorafenib treatment is 8.4 months (range 0.7-16.8); 59 patients (77%) remained on treatment at data cutoff. ORR in 69 RANO-evaluable patients was 64%, [3 CR, 41 PR (10 unconfirmed) and 19 SD] with a clinical benefit rate of 91%. The most common treatment-related adverse events (TRAEs) of any grade were hair color changes (75%), increased creatine phosphokinase (64%), anemia (46%), fatigue (42%) and maculopapular rash (42%). Two patients (3%) discontinued tovorafenib due to TRAEs. Updates from a longer follow-up on the 77 patients in arm 1 will be presented. Tovorafenib was generally well tolerated and showed encouraging evidence of antitumor activity in children and young adults with refractory BRAF-altered LGG.
IMMU-01. EVALUATING THE IMPACT OF CAR DESIGN ON THE TUMOR IMMUNE MICROENVIRONMENT AND ANTI-TUMOR RESPONSE IN SYNGENEIC GLIOMA MODELS
Authors: Dalia Haydar, Jeremy Crawford, Ching-Heng Chou, Cliff Guy, Zhongzhen Yi, Jaquelyn Zoine, Stephen Gottschalk, Martine Roussel, Paul Thomas, Giedre Krenciute
Journal: Neuro-Oncology (2023)

Abstract B7-H3 CAR T-cells have limited efficacy in immunocompetent mouse models indicating a suppressive role of the tumor immune microenvironment (TIME). In this study, we set to optimize B7-H3 CAR structure and examine the effects of CAR design on brain TIME. We generated a panel of second-generation B7-H3-specific CARs with different transmembrane (CD8, CD28), costimulatory (CD28, 4-1BB), and activation (ζ, mutζ) domains. We then compared the cytolytic activity, expansion, and anti-tumor activity of T-cells expressing these CARs. Results showed that T-cells expressing B7-H3 CARs with CD28 transmembrane/costimulatory domains have superior efficacy in vitro. Yet, providing optimized costimulation and signaling did not induce superior anti-glioma efficacy of B7-H3 CAR T-cells in vivo. Additionally, incorporating 4-1BB signaling into CD28-based CAR T-cells by expressing 4-1BBL on their cell surface enhances the therapeutic efficacy and persistence of B7-H3 CAR T-cells in vitro. However, transgenic expression of 4-1BBL in CD28-based CARs was not associated with further enhanced anti-glioma efficacy of B7-H3 CAR T-cells in vivo. Next, using high-dimensional flow cytometry and spatial transcriptomic analyses, we show that suppressive tumor-associated macrophages (TAMs) infiltrate tumors in non-responder mice and they predominantly surround the tumor edges. Additionally, minimal T-cell infiltrates were observed in these tumors with predominantly exhausted and dysfunctional phenotypes. Analysis of gene-expression signatures early after CAR T-cell treatment revealed that tumors treated with CD28-based CARs differentially upregulate genes associated with inflammatory myeloid responses. While treatment with other signaling domains’ containing CARs upregulates pathways predictive of suppressive TAM and regulatory/dysfunctional T-cell responses. We show that global depletion of brain macrophages using CSF1R inhibitor exacerbates CAR T-cell anti-tumor activity. In summary, our results show that specific CAR domains induce an early inflammatory immune hub predictive of potent anti-tumor responses. Additionally, inflammatory macrophages are needed for successful CAR T-cell activation and anti-glioma responses.
RARE-04. DEVELOPMENT OF A PLATFORM TO PROFILE MICRORNA IN CEREBROSPINAL FLUID FROM PATIENTS WITH INTRACRANIAL GERM CELL TUMORS
Authors: Joanna Gell, Jody Therieault, Patrick Ng, Ching Lau
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Current diagnosis of intracranial germ cell tumors (iGCTs) utilizes alpha fetoprotein (AFP) and chorionic gonadotropin (β-HCG) as biomarkers in the blood or cerebrospinal fluid (CSF). Two thirds of iGCTs are marker negative and AFP/HCG are not specific to iGCTs. Thus, there is a need to develop other biomarkers to improve the diagnosis of iGCT. Two microRNA (miRNA) clusters, miR-371-373 and miR-302/367 have previously been identified as biomarkers for extracranial GCTs and preliminary data from our lab and others confirmed their potential utility in iGCTs. However, the optimal way to profile miRNAs in CSF is not fully established. Two commonly used methods are real-time polymerase chain reaction (qPCR) or droplet digital polymerase chain reaction (ddPCR). METHODS CSF samples were obtained from biorepositories at Connecticut Children’s and through the Children’s Brain Tumor Network. Cell culture media from an embryonal carcinoma cell line was used as positive control. MicroRNA was extracted from 50uL of CSF, reverse transcribed into cDNA and pre-amplified. Samples were then diluted 1:5 for qPCR and 1:10 or 1:50 for ddPCR. RESULTS We profiled the CSF from 6 germinomas and 4 non-germinomatous, including two mature teratomas. Additionally, we profiled CSF from two non-iGCT brain tumors and two leukemia patients, as non-iGCT controls. For qPCR, raw CT values were evaluated with CT &amp;lt;35 considered detectable. Both platforms, qPCR and ddPCR were able to detect miR-371-373 and miR-302/367 in malignant iGCTs, including marker negative germinomas. miR-302/367 cluster showed varying expression in non-iGCT samples. CONCLUSIONS We were able to use low input (50uL) of CSF to identify markers of malignant iGCT, the microRNA clusters miR-371-373 and miR-302/367. Both platforms were able to identify the microRNAs. More samples will need to be profiled to evaluate which platform ddPCR or qPCR is best to move forward towards a clinically validated platform.
DIPG-12. OUTCOMES IN PEDIATRIC MALIGNANT CENTRAL NERVOUS SYSTEM TUMORS UTILIZING TEMOZOLOMIDE, BEVACIZUMAB, AND IRINOTECAN
Authors: Sarah Reel, Natasha Pillay Smiley, Trent Hummel, Adam Lane
Journal: Neuro-Oncology (2023)

Abstract High-grade glioma (HGG) and diffuse intrinsic pontine glioma (DIPG) are the most common high-grade glial tumors in pediatrics. Hummel et al. assessed the feasibility of bevacizumab (BVZ) ± temozolomide (TEM) with radiation, followed by BVZ, irinotecan (IRO) ± TEM. The regimen conferred no survival benefit to patients with DIPG. The study was limited by sample size. Further defining efficacy of this therapy is important. We aimed to examine the outcomes of patients with HGG and DIPG treated with BVZ, IRO, and TEM. This is a retrospective review of patients treated at Cincinnati Children’s Hospital from 03/2005 to 10/2022. We examined progression-free survival (PFS) and overall survival (OS). Descriptive analyses were used to examine age, sex, diagnosis, and tumor location. 47 patients were treated with BVZ, IRO ± TEM. Patients were 55% female and 45% male. Average age at diagnosis was 12 years. The diagnoses included patients with HGG (45%), DIPG (51%), and other tumor types (4%). 79% of patients were treated at initial diagnosis with the regimen of BVZ in addition to IRO ± TEM. 21% of patients were treated at progression. Median OS for patients with DIPG and HGG was 12.4 months and 35.9 months, respectively. 3-year OS for DIPG was 10.8% (SE 7.2%) and for HGG it was 48.6% (SE 11.0%). Median PFS for DIPG and HGG was 7.7 and 19.0 months, respectively. 1-year PFS for DIPG was 31.9% (SE 10.7%). For HGG it was 65.6% (SE 10.6%). 3-year PFS for HGG was 20.2% (SE 9.0%). The limitations of this study are that newly diagnosed and recurrent patients are included and the study does not examine radiologic and biologic data. Results from this study show promising data for OS and PFS. Additional studies are needed to further examine larger cohorts of patients to demonstrate survival benefit from this regimen.